The soybean, Glycine max, is one of the major economic crops grown worldwide as a primary source of vegetable oil and protein. Growing demand for low cholesterol and high fiber diets has increased soybean's importance as a food. Over 10,000 soybean varieties have now been introduced into the United States, of which a limited number form the genetic base of cultivars developed from hybridization and selection programs. Johnson and Bernard, The Soybean, Norman Ed., Academic Press, N.Y., pp. 1-73, 1963.
Soybean cyst nematode, (SCN, Heterodera glycines (HG) Ichinohe) is the single most damaging pest affecting soybean in the U.S. as well as in most of the other top soybean-producing countries of the world. The estimated yield reduction in the United States was between approximately 2.9 and 3.4 million tons in 2003 and 2004, which resulted in an estimated annual loss of approximately $1.5 billion. Wrather et al. (2001); Wrather and Koenning (2006). The SCN phenotype is a very complex trait, which is controlled by multiple genes, both recessive and dominant. Concibido et al. (2004). SCN phenotyping is time consuming, cost and labor intensive.
SCN infection causes various symptoms that may include chlorosis of the leaves and stems, root necrosis, loss in seed yield, and suppression of root and shoot growth. The aboveground symptoms of SCN infection are not unique to SCN infection, and could be confused with nutrient deficiency, particularly iron deficiency, stress from drought, herbicide injury or another disease. The first signs of infection are groups of plants with yellowing leaves that have stunted growth. The pathogen may also be difficult to detect on the roots, since stunted roots are also a common symptom of stress or plant disease. Adult females and cysts of SCN are about 1/32 inch long and, thus, visible without magnification. Observation of adult females and cysts on the roots is the only accurate way to detect and diagnose SCN infection in the field.
The presence of SCN is usually not obvious at the time of initial soil infestation. The SCN population density must increase in the soil until it is sufficient to cause above-ground symptoms on plants or a decrease in yield. Population densities may take several years to reach significant numbers. Thus, current SCN damage is the result of infestations that have been growing for several years. Although soybean is the primary host of SCN, other legumes can serve as hosts, for example: green beans, snap beans, dry beans, red beans, lima beans, mung beans, bush beans, Adzuki beans, garden peas, and cowpeas. There are thirty days in the SCN life cycle. Thus, a single growing season encompasses multiple generations of the parasite. Moreover, SCN eggs may remain intact in soil for several years before hatching.
In the past, an SCN population was given a “race” designation by comparing its reproduction on a set of four soybean germplasm lines with that on a standard SCN-susceptible soybean cultivar. The most commonly used race scheme identified 16 races of SCN. The race designation allowed nematologists and soybean breeders to share information about the ability of certain SCN populations to reproduce on soybean varieties that contain certain genes for resistance to SCN.
In 2003, the HG Type Test was developed to replace the race test. This new test includes seven sources of resistance (germplasm lines) and the results are shown as a percentage, indicating how much the nematode population from a soil sample increased on each of the seven lines. This test indicates which sources of resistance would be good for a particular field being tested, and which would be poor. Since the genetic sources of resistance are currently limited in commercially available soybean varieties, it is important to rotate these “sources of resistance” to delay the build-up of a virulent SCN population.
Shortly after the discovery of SCN in the United States, sources of SCN resistance were identified. Ross and Brim (1957) Plant Dis. Rep. 41:923-4. Some lines, such as Peking and PI 88788, were quickly incorporated into breeding programs. Peking became widely used as a source of resistance due to its lack of agronomically undesirable traits, with Pickett as the first SCN resistant cultivar released. The recognition that certain SCN resistant populations could overcome resistant cultivars led to an extensive screen for additional sources of SCN resistance. PI 88788 emerged as a popular source of race 3 and 4 resistance, even though it had a cyst index greater than 10% (but less than 20%) against race 4, and Peking and its derivatives emerged as a popular source for races 1 and 3. PI 437654 was subsequently identified as having resistance to all known races and its SCN resistance was backcrossed into Forrest. Currently, there are more than 130 PIs known to have SCN resistance. PI 209332 and PI 90763 are other exemplary SCN resistant soybean breeding lines. Not all varieties with the same source of resistance have comparable yields, nor do they respond identically to SCN.
Resistant soybean varieties are the most effective tool available for management of SCN. SCN densities usually decrease when resistant soybeans are grown because most SCN juveniles are unable to feed and develop on the roots of the resistant varieties. However, in any naturally infested field, a few SCN juveniles (<1%) will be able to reproduce on the resistant varieties currently available. The number of SCN juveniles that can reproduce on resistant soybean varieties can increase when resistant varieties are grown repeatedly. Eventually, the SCN population may be able to reproduce as well on a resistant variety as a susceptible variety if SCN-resistant soybeans are grown every time soybeans are produced in an infested field. Fortunately, the number of SCN juveniles that can reproduce on resistant varieties declines when susceptible soybean varieties are grown because these nematodes do not compete well for food with the other SCN juveniles in the soil that cannot feed on the resistant varieties.
SCN race 3 is considered to be the most prominent race in the Midwestern soybean producing states. Considerable effort has been devoted to the genetics and breeding for resistance to race 3. While both Peking and PI 88788 are resistant to SCN race 3, classical genetics studies suggest that they harbor different genes for race 3 resistance. Rao-Arelli and Anand (1988) Crop Sci. 28:650-2. Race 3 resistance is probably under the control of three or four different genes. Id.; see also Mansur et al. (1993) Crop Sci. 33:1249-53. One major SCN resistance QTL that maps to linkage group G is rhg1. Concibido et al. (1996) Theor. Appl. Genet. 93:234-41. Other SCN resistance QTLs map to linkage groups A2, Cl, M, D, J, L25, L26, and K. Id.; U.S. Pat. No. 5,491,081. SCN resistance QTLs behave in a race-specific manner, at least by accounting for different proportions of the total phenotypic variation with respect to different SCN races. Concibido et al. (1997) Crop Sci. 37:258-64. However, the rhg1 locus on linkage group G may be necessary for the development of resistance to any of the identified SCN races. But see Qui et al. (1999) Theor. Appl. Genet. 98:356-64.
Markers that are linked to SCN traits include RFLPs, SSRs and SNPs. The SNP markers identified in this disclosure can be used to do SCN genotyping to support a breeding program. Using the presently disclosed SNP markers to perform SCN genotyping in support of a breeding program provides: cost and time savings, early selection of desired progeny, and more accurate and rapid commercialization of SCN resistant soybean varieties.